tag:notobiotica.posthaven.com,2013:/posts noto|biotica 2017-11-16T20:39:15Z noto|biotica tag:notobiotica.posthaven.com,2013:Post/1205378 2017-11-15T00:35:38Z 2017-11-16T20:39:15Z The rarity problem in Australian taxonomy

"Anybody could do that," replied the young fellow contemptuously. "I want to distinguish myself."

"Then I'll tell you what you'll do, Moriarty. Take a narrow branch of some scientific study, and restrict yourself to that. Say you devote your life to some special division of the Formicae?"

"The what?"

"Formicae. The name is plural. It embraces all the different species of ants."

"Why, there's only about three species of ants altogether; and there's nothing to learn about them except that they make different kinds of hills, and give different kinds of bites. That sort of study would about suit you. Fat lot of distinction a person could get out of ants."

- Tom Collins, Such Is Life (1903)

Moriarty could be forgiven for thinking there were only three species of ants on Runnymede Station. Those were the common species, the ones he saw every day. Moriarty didn't know that most species in any taxon are naturally rare.

Ecologists know about rarity. They do an exhaustive survey of some group of organisms on a study site, and find that there are a few very abundant species and a "long tail" of much less abundant species. They build a rank-abundance diagram (https://en.wikipedia.org/wiki/Rank_abundance_curve) from their results.

For ecologists, those many rare forms are a statistical nuisance, and there are hundreds (thousands?) of published articles in which the rare forms have been deliberately ignored: "Species represented by 10 or fewer individuals were excluded from the analysis."

The rare forms can also discomfit the ecologist with a taxonomist on tap. The latter has no trouble naming the abundant species, because these were collected and described long ago. But when the taxonomist sends the ecologist a final species list, many of the rare forms that were collected only have code names like "Improbabilidae sp. 1", because they hadn't been seen before. By anyone.

The rank-abundance relationship applies to terrestrial, freshwater and marine taxa. It's one of the principal obstacles to naming and describing the entire Australian biota, but it's not often discussed.

Think of taxonomy as the discovery, documentation and classification of life. The latter two activities can increase more or less proportionately with resourcing. The more money you put into training and funding taxonomists and systematists, the more species get properly documented and classified.

Discovery is different, because the amount of money needed to collect specimens increases with the rarity of the species. On day 1 of a field trip you can find 50% of the species at a study site. As time goes on, the rarer species drop one by one into the collecting bucket, but even after a week the species accumulation curve (https://en.wikipedia.org/wiki/Species_discovery_curve) may not have levelled off.

I'm currently working up a set of Tasmania's rarest millipedes, some of which are only known from single specimens. Not only are these species naturally rare, they have jackpot distributions on a small spatial scale. If I'm lucky, I'll find a jackpot of several adults in a metre-square patch of forest litter. Most of the time I'm unlucky. I'll go to the only known locality (usually it's a revisit to one of my previous sites) and won't find the target species, just new locality records for more abundant ones. So I keep looking. Field trips cost time and money, and these rare forms are costing far more than their more abundant congeners and confamilials did.

Mine is nearly a "best possible collecting" scenario, because millipedes in Tasmania can be collected in the right life stage at any time of year. Think of all the rare Australian species which are only findable or recognisable when the the season or the weather is right!

Bob Mesibov

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Bob Mesibov
tag:notobiotica.posthaven.com,2013:Post/1203542 2017-11-06T04:36:32Z 2017-11-06T10:31:29Z Storing and sharing data
One aspect of our research that I don’t remember seeing much comment on in relation to the Decadal Plan currently being prepared (https://www.science.org.au/support/analysis/decadal-plans-science/biosystematics-taxonomy) is the safe long-term storage and sharing of data.
I was reminded of this by a very recent editorial by Theresa Culley in Applications in Plant Sciences 5(10): ‘The frontier of data discoverability: why we need to share our data’ (see http://www.bioone.org/doi/abs/10.3732/apps.1700111).
 
She points out that not only SHOULD we make data widely accessible, it is now often required by granting bodies and journals.
To quote from her abstract, there are good reasons for depositing data in permanent repositories:
 
‘(1) it prevents data loss due to accidents, theft, or death of the researcher; (2) it enables published research to be reproduced by others; (3) publications associated with accessible data sets can have higher citation rates; (4) deposited data sets are increasingly recognized for scholarly recognition and professional advancement; and (5) stored and accessible data can be used in the future for projects that are unanticipated today’.
 
Her article is based on the American situation, but the main points are also very applicable for Australasia.
She raises various questions about procedure such as: Who should set up such data repositories? Who should be responsible for seeing that data are stored in a suitable format and with appropriate metadata to make them intelligible in future? Who should pay (always a big question) for these repositories and for ongoing curation of data to ensure continuing accessibility?
 
Current examples of data repositories that have been widely accepted as useful are GenBank and EMBL for sequence data. Dryad (http://datadryad.org/) is another example. 
 
It would be useful if the Decadal Plan addressed at least the general question of data repositories in our field of research and what we might aspire to achieve in the next decade. Is data storage another role for the proposed coordinating body for biosystematics and taxonomy? Or is there enough activity in other parts of the world for us to just use what is being set up there?   
 
 
Karen L. Wilson AM
 
Honorary Research Associate, National Herbarium of New South Wales
Adjunct Associate Professor, University of New England, Armidale, NSW
Secretary, General Committee, International Code of Nomenclature for Algae, Fungi & Plants   
 
Botanic Gardens & Centennial Parklands
T +61 (02) 9231 8137 | E karen.wilson@rbgsyd.nsw.gov.au
Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney NSW 2000, Australia
 
 
 
 
 
 
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Karen Wilson
tag:notobiotica.posthaven.com,2013:Post/1202094 2017-10-31T01:58:26Z 2017-11-01T05:11:24Z Taxonomic Implications of Decadal Plan

Perceptions of a Sociopathic Taxonomist

Disclaimer: At the outset I will proffer my apologies to those who know me. If anyone asks, I completely understand if you choose to deny that you’ve ever had any association with me, implied or otherwise. The views upheld in this brief note are those of the author alone, not a single other person on the face of the Earth. God help us all if there’s others like this.

“The outcomes and recommendations in this report are aimed at informing the primary stakeholders of Australian astronomy of the current status of the field, the strengths and progress made by the Australian astronomy community, the big scientific questions that Australia is best equipped to answer, and the infrastructure and capability priorities for the future needed to realise this ambition.”

After reading the Decadal Plan for Australian Astronomy (DPAA), I couldn’t help but feel underwhelmed by its content as I walked away from it. Out of some 80 pages, half a dozen, at best, actually outlined any astronomical achievements, as it were, over the preceding 10 year period, and for the next 10 as proposed within the current plan. The underlying emphasis throughout the documentation, from my reading at least, was a focus on infrastructure; incessant reiteration; industry subservience; over-generalized, content-free catch-phrase statements; and collaboration on nationally decentralised projects (i.e. ownership no longer belongs specifically to Australia). One of their own stated objectives was “funding a skilled workforce is critical to exploit the next generation of scientific infrastructure”. That’s all well and good, but the sceptic in me couldn’t get past the feeling that the astronomy discipline has committed the very sin that our working groups have discussed as being one to avoid at all costs – reducing bureaucratic nonsense and other distractions and letting the taxonomists just do their research (not to mention the establishment of long-term research career paths within our industry as well). From what I see, they have devolved from being an astronomy-centric discipline to an institute comprising physics experts who are now acting as engineers for producing low-cost, high-end infrastructure for industry purposes/gains, astronomy hopefully getting some crumbs somewhere down the line:

“The scale of future astronomical facilities demands skills, expertise and technologies beyond the current capabilities of Australia’s academic community. Meaningful industry engagement is required to build partnerships that will design, develop and produce the next generation of astronomical instruments, and to harness the innovation flowing from fundamental research for commercial application.”

Whilst I am well aware that they don’t tell the whole story, and many jobs have been created within the industry, just what are those jobs? The examples they provided of career paths that astronomy PhD graduates can hope to realise all indicated that, after a short initial involvement in the field of astronomy, they invariably go off into other fields e.g. medical, renewable energies. Whilst those are commendable pursuits within themselves, it is hardly a ringing endorsement of Astronomy as a long-term career path, or indeed, the success of their decadal plan as it actually relates to Astronomy. The research focus, where it is broached, is centred on infrastructure and the acquisition of excessively large amounts of data. A glaring omission from the DPAA, Round 2, is any analysis of what existing members of the industry think of their positions, research, prospects and the success of the DPAA itself. Could make for interesting reading.

“The development and effective utilisation of the ASVO and other data-related initiatives will require the astronomy community to foster a new type of scientist, dedicated to data-intensive activities—managing, curating, manipulating, processing vast volumes of data, extracting information from it and making data and information available and accessible to other scientists. Currently these scientists are largely missing from the astronomy community and a challenge for the next decade will be to train such scientists and create career paths for them.”

This sounds a lot more like tech jobs than research positions, as far as the nuts and bolts of astronomy are concerned that is. Forgive me for suggesting that the independence of the discipline has been compromised. Whilst there’s nothing wrong with tech jobs (and we certainly need more in our own science), before anyone gets indignant, we all recognise, I’m sure, that there is an ongoing need for the researchers as well.

On the other, more positive hand, however, the DPAA does purvey an ethos which I feel is almost completely lacking in the taxonomic sphere – they do present a strong sense of self-appreciation and self-value. They very strongly emphasise that they are important as an industry and that their skills are of a high standard, and those skills require a significant investment in education to acquire and apply. For my money, this is the taxonomic industry’s weakest link. I simply cannot get over what I have experienced as being the innate sense of unimportance most taxonomists appear to have. I was once told by a colleague that “this stuff could be done by a trained monkey.” Another said “what we do is nothing more than natural history.”

Well! I’m not sure I am in 100% agreeance with those statements. Maybe I’m even stupider than I originally thought, my perceptions of minimal intellectual competence being nothing more than misdirected self-indulgence. After writing this, there will no doubt be a lot more who agree with the latter. But honestly, why work in the industry if the previous statements are representative of your perspective? More on this later.

Back to the positives: there were three other salient points that were raised in the DPAA which I feel it would behove the ‘Australian Taxonomic Organisation’ (ATO) to adopt:

  • Australia’s astronomical research excellence rests on continued partnership between astronomical observatories and the universities.

  • The professional Australian astronomy community has undergone significant growth in the past decade with a rise in research capacity across the entire community, particularly in the training of higher-degree students and early-career researchers.

  • In the next decade, greater collaboration and partnership among astronomy research organisations and astronomy outreach providers is essential for expanding the public impact of astronomy.

It’s not really a lot out of 80 pages – just saying! Enough of dissing Astronomy though. Time to look in our own backyard.

Taxonomy 2028: Well! Where DO we go from here?

“By 2028, we will have a quality assurance and accreditation system for taxonomy and systematics across Australia and New Zealand.”

This statement (not mine by the way) was relayed in one of the brainstorming sessions Kevin held recently. If I were awarding prizes for the best idea presented, then I think this one would get it.

Quality control and an actual recognition of expertise. That would be nice. If we achieve nothing else, let’s at least aim for that.

It’s interesting to read all the blogs that have thus far been posted on this site. Some are egocentric (as is mine), some are left-field, many are subject-specific, some are measured, some are on the mark and others are unrealistic - at least according to my set of value judgements and set of experiences. Each of you will undoubtedly see it differently. How do we assemble all these differing suggestions and ideas to become an end product with which all stakeholders are at least reasonably satisfied? At the end of the day, what do we collectively want those end products to be and who will use them? More importantly though, I feel, is what to we want our industry to look like a decade from now? What do we want a position description for a taxonomist to look like a decade from now?

That’s the key, I think (pun noted). Collectively! Not as individual researchers. You know! “United we stand…..”. (Isn’t it ironic that it all seems to come back to the lumpers vs. splitters debate?)

The taxonomic/systematic ‘industry’ is a very diverse one – naturally. We study diversity. But just what IS that level of diversity? Scientists had enough problems in agreeing on how you define what a species or taxon is/was when they were only dealing with morphological characters. How do we define that which is arbitrary now? Therefore, on what basis do we enumerate it? Depending on the degree of genetic resolution that you use, each and every one of us is potentially a unique taxon. Only clones would be spared this ignominy, and I only know a few of those, albeit the evil ones. Why not just give us each a number and set us to work on the estate? I’m not entirely convinced (more than happy to be proven wrong) that we can engage the interest and concern of the general public by entreating them with statements like: ‘2,340 barcodes will become extinct if that development goes ahead’. Makes you feel all warm and fuzzy, doesn’t it? Makes the argument for the use of scientifically-generated names over common names a bit questionable for the everyday punter.

Taxonomy seems to have devolved into the art of ignoring multiple elephants in the room whilst simultaneously developing new and more complex technologies with which to confuse the science, and all the while spewing forth copious, more meaningless data for which storage issues constantly arise.

‘We have ALL this data!’

And….?

Look at it this way - within the lifespan of this proposed Decadal Plan, somewhere in the order of 130 million hectares of land will be cleared globally (based on current rates and assuming no deviation from that rate). That is 1.3 million km squared. That’s about 70% of the state of Queensland, assuming it was completely covered in vegetation to start with. So just how are we assisting conservation goals again? That is one of our mantras after all. Likewise, how on earth do we define rarity under the genetic code regime? Surely that answer will be as diverse as the number of geneticists out there. All this data. No more answers. Fewer workers.

There seems to be a hole in the taxonomic bucket, Dear Liza, Dear Liza (my sincere apology to anyone who IS actually named Liza and who may end up reading this). A lot of posts here, and responses to the brainstorming sessions, highlight what projects the respective authors consider can be achieved by 2028. Many present a wish list. Good thing the draft document will be ready just before Christmas. In the infrequent event that my left brain cell interfaces with my right brain cell, I can’t help but thinking, fleetingly, that some of the important questions SHOULD be:

How is it funded? (I know – Duh?)

How is it staffed? (Ditto)

Who will train the staff?

What are we producing?

Why are we producing it?

Who really wants it?

Who really cares?

Will the products we are producing now, and the new technologies we are using, still have relevance in 2028?

Come 2028, will our industry be well poised to conduct a second Decadal Plan?

What will a position description look like in 2028? (This is particularly relevant if we refer to our stated objective of an increase in taxonomic positions.)

How do we expect to convince politicians, the general public, and even other scientists that our research is important if we can’t agree on anything (present a united front), and if we are perceived as being a discordant discipline applying arbitrary principles to an ever-shrinking diversity base? How do they gain TRUST in our science and its outputs, and the quality thereof?

On that note – quality assurance – just what is it about taxonomic science that impels us to cut our own throats? I am going to create a LOT of bad blood by suggesting this because it has seemingly become the driving force behind our vocation in recent years, and now a government initiative (why do you suppose that is?), but why are we pushing so many resources into citizen science at the expense of resuscitating/replenishing our own profession? This comes back to the whole self-value/self-appreciation factor that the DPAA got right. Citizen Science, from memory at least, wasn’t addressed in the DPAA. Don’t misrepresent me, however. I do believe they have roles to play, but I think we need to adopt those with more of a self-preserving outlook.

L: Why are there so few taxonomists now employed in Australia?

H: “Because there aren’t the jobs”

L: “But there won’t be either if there’s a workforce doing it all for free”.

H: “That’s OK! We just need someone to train the public”.

L: “But who trains the trainer, and who does the research if the only qualified people are training volunteers? No-one is being professionally trained in this discipline anymore!”

H: “Why not?”

L: “Because there aren’t any jobs”.

Pass the bucket, Liza.

Why are we so amenable to giving everything, especially our hard-fought knowledge, away for free, or next to it? Just because many of us are employed with public funds? If that’s the logic, then no goods or services coming from government departments should incur a charge. Yeah, Right! Why do we blithely accept our lot and hand over our intellectual productivity for public manipulation and misrepresentation just because we’re paid from the public purse? Don’t we have a responsibility to also act as custodians of that information/data? After all, isn’t it allegedly generated in the national interest, much of it feeding into our longer term heritage and prosperity? Just saying!

What good does it do for us to push for university placements if the jobs aren’t there at the conclusion? Are we to become more like the astronomists, producing high-quality graduates for other industries? (What an absolute waste of time for the few experts that we do have). What incentives exist for students to study in this profession, apart from passion? Is there a career path? Is it one where you can still be conducting research at the upper limits of progression? Do students  want to spend the best part of a decade undertaking hard work, often under trying circumstances, to end up just handing that expertise over to the public on a plate (that plate being some form of bright, shiny, multi-functional technological marvel which will then have to be replaced almost immediately with whatever technology has been freshly developed at that point), only to have to spend the rest of their career trying to convince the latter that they don’t actually know more than the former (in most cases)?

Really! Why do we sell our science so short? Personally, I consider that to produce quality taxonomic output requires a specific set of skills, the combination of which is not as commonplace as some proclaim (and certainly beyond that of a trained monkey). What is our currency if it isn’t that particular set of skills? If any Joe Average can come off the street and do what we do, and just as well as those who have been trained for years, then why are we bothering with a Decadal Plan? Why WOULD the government bother to create FTE’s and invest funding? Pretty basic really. If you want the government or private industry to invest dollars, you have to have something to offer them that they can’t get elsewhere. So what are we doing/producing that stakeholders can’t get elsewhere?

Something I find to be a particularly noteworthy result emerging from the roadshow brainstorming sessions was the relatively minimal input of ideas on taxonomy itself. Of the 150 summary points recently circulated, only 11 (7·5%) pertained to the combination of the categories of Taxonomy, Nomenclature and Molecular Tools (all the stuff we actually DO), and even then some of those had considerable overlap. Even if you consider the individual contributions themselves, of the 418 put forward, only 36 (8·6%) gave consideration to those three factors. This can be viewed any number of ways, but maybe it’s a positive. Maybe, collectively, we consider taxonomic endeavour in and of itself to be in reasonable shape. Is it just the infrastructure, governance and resourcing of the industry that has fallen into a state of untenable disarray?

Given that no-one is likely to have persisted and read this far (I know I wouldn’t have), I’ll self-preservingly finish with an explanatory note.

Originally, I wasn’t going to bother having any input into this process. I know. Shame on me. It was remarkable, however, how many colleagues shared that viewpoint, considering it to be a waste of time, a pointless exercise producing a document that has little bearing on reality. I figure there’s plenty enough work to be done with the material I’ve got available to me – enough to see me to the end of my career and beyond. Of course, that is a self-centred outlook and one which only serves to achieve my objectives. A different perspective is required however. The task is bigger than me. It’s bigger than you. We all have our part to play, and whilst we may not always agree with each other, we need to be pulling in the same direction as a team. A good friend of mine has spent many years studying for a career in taxonomy. Not only that, the enthusiasm and infectious appetite they have for the science is exemplary and refreshing. If I abstain from involvement, if any of us do, then we rob people like that of their chance to realise a goal, a dream. That’s not fair and it’s not right! So this is my 10₵ worth; my 15 minutes.

This is about the future. There is extraordinary potential in this industry. There is still heaps of work to be done, particularly once you get past the flora and megafauna into studying the important organisms (that should get a reaction). I exhort the planning team to keep sight of what we are about and what we are producing. Let’s do our best to not resorting to prostituting our science as some form of quick fix to a seemingly insurmountable conundrum. We need our stakeholders to come up to our level, not allow them to drag us down to theirs. Above all, we need to keep the science real and avoid the trap of being caught up in the infinite quest to align our output with technology. We’ll never catch up and there’s still more than enough baseline taxonomy to be done to feed into all those wonderful databases and programs. At present, we’re creating products based on a fraction of the potential data which remains to be collected. Let’s focus on that at least as much as we focus on new ways of presenting existing data over and over again.

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Nigel Fechner
tag:notobiotica.posthaven.com,2013:Post/1200185 2017-10-23T03:46:18Z 2017-11-02T18:48:17Z Criteria for prioritisation of invertebrate taxonomy

From A/Prof. Michael Braby, Visiting Scientist, Australian National Insect Collection, based on recommendations from the paper Biosystematics and conservation biology: critical scientific disciplines for the management of insect biological diversity. Austral Entomology 55:1-17 (see http://onlinelibrary.wiley.com/doi/10.1111/aen.12158/abstract)


Given finite resources for biosystematics, we argue that at least two criteria be considered for selection of invertebrate groups for prioritisation for taxonomic focus and their application in conservation biology: (1) the taxon is reasonably well known taxonomically (i.e. total inventory is estimated to be 90% complete, and/or morphospecies have been circumscribed through the availability of parataxonomists and well-curated reference collections); and (2) the taxon is known to be informative as bioindicators. 

Here are our main visions for taxonomy from a stakeholders perspective (biodiversity conservation):

  1.  Increased investment in taxonomic research capacity (of prioritised taxa) to systematically catalogue known species and describe new species, including university training and resources for museum collections, curation, digitisation of material (including type specimens), DNA sequencing and development of taxonomic databases on the Internet.
  2. Greater attention towards molecular genetic methods, such as DNA barcode technology and application of genomic data through next-generation sequencing together with population genetic studies of species will assist with rapid identification of field samples, especially where morphospecies approach is used for some prioritised taxa, as well as recognition of conservation units within species. This technology should not be used at the expense of traditional taxonomy, but rather complement it.
  3. Complete reconstruction of the evolutionary history or tree of life, which will form the framework for the development of reliable guidelines and conceptual basis as to how phylogenetic diversity can be incorporated into biodiversity conservation planning compared with traditional measures, such as species richness, endemism and threatened species.
  4. Development of national databases to document the spatial distribution of species, and predictive spatial modelling of biodiversity. The ALA and related activities, such as the Australian Natural Heritage Assessment Tool, are excellent government-funded initiatives in the field of bioinformatics and are currently the best platforms on which to build at the national level.
  5. Increased capacity-building through greater participation of citizen science programmes in collecting spatial and temporal data and indices of relative abundance of species. These data can then be used in conjunction with databased vouchered specimens for evaluation of geographical range, phenology and conservation status of threatened species. Networks consisting of government agencies, NGOs, scientists, community groups, natural history societies and volunteers are likely to be the future for the conservation management and monitoring of insect biodiversity in Australia.


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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1197991 2017-10-13T07:19:40Z 2017-11-15T07:51:11Z Direct action

A suburban mall, 2 pm. Mothers and grandmothers sit chatting in the shade. Toddlers squat together in a sandbox, their sun-hats almost touching. The lunchtime business crowd has gone back to their offices. A waiter wipes down the vacant outside tables and pushes chairs back into place. A white ibis (Threskiornis molucca) perches on the rim of a rubbish bin.

Inside the Café Vittoria, a young woman in sunglasses sits with a latte, idly flipping the pages of a magazine. She's been waiting half an hour and is running out of patience. The candle stub she's brought with her is burning low in an ashtray on the table. She wonders if she has another in her handbag.

Into the café sweeps an older woman, smiling and laden with shopping bags. Looking around the café, she spots the candle-lit table and bustles over, dumping her bags on and under the table's empty chairs.

"Whoosh!" she says, sitting down to face the younger woman. "Ontogeny recapitulates phylogeny."

"But morphospace is boundless," replies the other, coolly.

Passwords having been exchanged, the women shake hands and murmur "Luz" in unison. Thus begins another clandestine meeting of agents from the League of Unemployed Zoologists, LUZ, whose acronym means "light" in Spanish and whose emblem, the candle, symbolises the vulnerability of zoological knowledge.

"Life in Sydney has been good to you, I see", remarks the younger woman with a hint of sarcasm, nodding towards the shopping bags.

"They're empty boxes in those bags, sweetie", replies the other. "Part of my disguise. What's your UID? I'm Patiriella, Marine Section."

"So I was told. Austrochorema, Freshwater. You're late."

"Not by much. What do you have from Melbourne?"

Austrochorema sips her latte. "A little. Our colleague at Museums Victoria slipped a plea for donations into a squid being loaned to the Smithsonian."

"Really? Which part of the squid?"

The younger woman frowns. "Can we please stick to business?"

A waiter heads their way. "I'll have a long black," calls Patiriella, and the waiter retreats. "Sorry. Anything out of La Trobe?"

"Nothing good,'" replies Austrochorema. "The School of Life Sciences got wound up. Long-contract staff are going into the new Department of Resources, Econometrics and Accountancy Development.'

"A fitting acronym," observes Patiriella. "I don't suppose they'll be offering anything on invertebrates."

"Hardly. Listen!" Austrochorema leans forward, suddenly animated, speaking in a fast whisper. "There's a plan out of Edith Cowan. Do you remember the Bogong Incident, when millions of moths invaded Parliament House in Canberra?"

The conversation is interrupted by the arrival of the coffee.

"Of course," replies Patiriella, when the waiter is out of earshot. "How could I forget? Insects in the newspapers for days, ANIC footage on the TV news."

"This is bigger. Breeding colonies have been established at secret locations near Albany and two more are planned for the Launceston area."

"What is it? Another moth?"

"We aren't to know. There are hints, though. Conventional poisons won't help. The only way to control these things will be with an attractant, a pheromone tailored to this one, genetically modified disrupter."

Patiriella sighs. "I don't know. Terrorism seems so...extreme."

"This isn't terrorism," enthuses Austrochorema. "It's direct action. The Commonwealth just needs to be reminded of the importance of zoological expertise. Pheromone traps will be activated when our demands are met: full restoration of zoology faculties and courses at universities across Australia, return of ABRS funding to CPI-indexed 2015 levels, guest spots for soil zoologists on the ABC-TV gardening program..."

"I know, I've read the manifesto. But can we trust the bastards?"

Austrochorema smirks. "They'll keep their promises this time. If they want the beaches to be safe."

Patiriella's eyes widen. "I've heard nothing about this! And I'm in Marine Section!"

The younger woman breathes gently on the candle between them. For a moment, the flame grows. "We have friends overseas, Patiriella."

(To be continued, unless the Decadal Plan reverses the trends. If not... luz.)

Bob Mesibov

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Bob Mesibov
tag:notobiotica.posthaven.com,2013:Post/1196765 2017-10-08T13:44:17Z 2017-10-11T19:35:34Z Taxonomy 2028 Challenge: Let’s digitally image poorly known described species and undescribed species in an Australian Biodiversity Portal – the end-users perspective by Volker W. Framenau (Perth)

I am an invertebrate scientist publishing taxonomic and systematic studies predominantly on spiders. I am also an environmental practitioner conducting invertebrate surveys in Western Australia trying to identify spiders from often poorly sampled, remote regions.

I am therefore as much a taxonomist as I am an end-user. I am familiar with the taxonomic literature of described species in my area of expertise (and some other invertebrate groups such as millipedes and ants) and have little problems to identify species that had a very recent taxonomic treatment and for which biodiversity and distribution data is readily available (i.e. through identifies specimens in collections published in the Atlas of Living Australia).

What I need, as expert end-user, is a system that helps me identify a species that is not properly illustrated (i.e. historically named, but with poor original description) and those that are undescribed.

As end-user trying to protect rare species, I don’t need a Linnaean name for this, but I need to know if a species is potentially rare or widespread, which determines if it is subject to an environmental assessment or not. In Western Australia, a species does not have to be named scientifically to be protected by the Wildlife Conservation Act.

Imagine, I could find images of all undescribed and poorly described species online, with diagnostic images, i.e. all pedipalps of male spiders in ventral view for a family or genus side-by-side? Apply the ‘retrolateral’ filter, and then I get them all in a different view for identification. Or images of heads of undescribed ants of a genus side by side? Impossible by 2028? Of course not!

Check out www.antweb.org  and you can find thousands of images of ants (described and undescribed, the latter with morphocodes), can filter by bioregion, taxonomy and morphological view. Or closer to home, check out the Barrow Island QIM (http://www.padil.gov.au/barrow-island/search?queryType=all) funded by Chevron Australia as part of its biosecurity efforts for its Gorgon Project, that illustrates in access of 2,000 terrestrial invertebrate species, many with morphospecies codes. I have used this resource excessively for identifications of spiders and ants in the nearby Pilbara. Imagine a Barrow Island QIM for the whole of Australia, just better!

This of course will not work for all taxa, some cannot be easily identified by images alone, but for many it will work, as long as species-specific images are being presented (here the Barrow Island QIM falls short, at least for spiders).

There are three main elements that need to be developed for this:

  1. The database structure and gallery type web-design with appropriate filters for images that are meta-tagged for these filters.
  2. An Australia-wide pseudotaxonomic/morphospecies framework for undescribed species with unique species identifiers. This can be modelled on the Linnaean system, i.e. it will require ‘morphotypes’ to fix a morphospecies.
  3. Expert curators for specific groups, possibly at state-level, that oversea the addition of new species.

Addition of new species will likely be managed at the state level, so let’s think this through for WA and spiders. There are approximately 900 described species in the state, our best estimates of the total number of species is probably three times as much (round it up to 3,000). For arguments sake, let’s assume that about half of the described species have been recently revised and can be identified based on published revisions. That leaves us with ca. 2,500 to be illustrated online for identification (however, no reason to not also include described species by using the published images, copyrights permitting). Many of these will occur in the neighbouring states or even Australia-wide (Australia-wide, about 3,800 spider species are described of an estimated 10,000+ species).

This number for WA spiders is just about as much as the Barrow Island Quim has been done since 2004! Not only is it possible, it has actually been done.

Let’s now assume, like Antweb, an online image catalog is being contributed to by the whole scientific community, overseen by expert curators to guarantee taxonomic consistency of the system? For example, if I as environmental consultant with expertise identification skill find a species and cannot find it online, I submit standard images and the specimen to the ‘curator’ who simply has to upload the images, establish a morphotype and add distribution data to the database (maybe by IBRA region?). In a well-established online Contents Management System (CMS) this may take all put 15 min per species. It’s almost like the Encyclopedia of Life for undescribed species. Once it is set up with a core number of species for each taxon, I would hopefully again momentum. Imagine then, that museum curators use the system to identify new accessions, database these and the respective distribution data would be available on the ALA (which by then allows listing of the established morphotypes).

We would move from species description to species registration, which, of course, would ultimately enormously facilitate future taxonomic revisions.

Of course there will be errors in the system, but a species is only a hypothesis after all

We won’t be able to scientifically describe all invertebrate species by 2028, but we can document a large proportion of these within 10 years!

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Volker Framenau
tag:notobiotica.posthaven.com,2013:Post/1196680 2017-10-07T22:58:38Z 2017-11-01T18:19:52Z Sally Fryar

I am a fungal taxonomist, specialising in the marine and freshwater fungi of Australia. These are mostly ascomycetes and their asexual forms.

I completed my PhD at Flinders University in 1997 on the taxonomy and ecology of wood decay fungi (basidiomycetes), examining indirect effects of multi-species interactions. In 1998 I moved to Hong Kong as a postdoctoral fellow at the University of Hong Kong where I was introduced to the fascinating world of freshwater and marine fungi under the supervision of Professor Kevin Hyde. My research took me to various peat swamp forests, mangroves and streams in Borneo where I was a visiting fellow at the Universiti Brunei Darussalam. 

The challenge with studying marine and freshwater fungi is that species descriptions are scattered throughout the literature, often in obscure, inaccessible journals and with poor illustrations. While taking a career break to have children, I spent 10 years gathering as much literature as possible on marine and freshwater fungi, putting together a database on worldwide records of each species along with their descriptions.

My aim is to provide thorough, consistent, understandable descriptions of marine and freshwater fungi of Australia along with clear illustrations and images so that non-specialists are able to identify these species.

I often find new species and genera and I am in the process of describing and publishing a number of these along with phylogenetic analyses based on molecular data.

I am an adjunct senior lecturer at Flinders University where I do some teaching and molecular work.

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Sally Fryar
tag:notobiotica.posthaven.com,2013:Post/1195292 2017-10-02T05:06:53Z 2017-10-12T07:06:42Z Ensuring adequate communication between environmental consultants and taxonomists

From Stephen Ambrose, Director, Ambrose Ecological Services Pty Ltd


In general, there are two types of ecological consultant:

  1. Specialists who focus their activities on one group of taxa (e.g. birds, bats, reptiles, marine animals) or in one industry sector (e.g. mining, urban development).
  2. General Practitioners who don’t have a particular focus and work across a broader range of ecological consultancy issues at a more superficial level than specialist consultants.

Specialist consultants tend to keep abreast with the taxonomic and biosystematic changes in the taxa that are the focus of their interest.  They usually do this by following the scientific literature, attending conferences, and occasionally being the drivers of the taxonomic and biosystematic studies.

However, generalist consultants cover too broad an area to easily keep up with revisions of all taxa that they deal with during the course of their work.  It is this group of consultants who would benefit the most from better communication about these revisions.

While the onus is on individual consultants to keep up with these revisions, taxonomists could assist with facilitating communication with them.  One possible way of doing this in NSW would be for taxonomists and evolutionary biologists to send hyperlinks to the Ecological Consultants Association of NSW (the ECA) admin@ecansw.org.au to relevant online publications or websites.  The ECA’s Administration Officer would then forward this information to ECA members, either as a regular ECA Information Emails or as collated information in the ECA’s regular journal, Consulting Ecology.

There is probably an opportunity for taxonomists to receive information from ecological consultants, too, based on field work associated with development assessments, but I’m not sure how best to facilitate that interaction, especially as there is usually a commercial-in-confidence agreement between consultant and client.  There is also the likelihood that there will be less opportunity for this to happen with ecological consultants (in NSW, at least) spending less time in the field, and more time in front of the computer, under the new environmental legislation.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1193432 2017-09-24T10:15:53Z 2017-09-26T06:18:38Z Taxonomy 2028 Challenge: Recording Indigenous nomenclature

Australia’s first nomenclaturists were those who first settled country, and in doing so began to utilise our plants and animals for food, tools, shelter, medicines and ceremony. During the more than 50,000 years of living on and with the land, Indigenous people have developed a rich nomenclature for taxa used in these ways. In each language group, specific words are used for around 10% of plants in the area, sometimes with multiple words for one Western-accepted species when there are multiple uses or different life stages are used. With many language groups and many species across Australia, this is a very large body of knowledge.

With the historical and ongoing disruptions to traditional knowledge, languages and cultural activities, many of these words, and their connections to knowledge, are endangered. This loss would be a tragedy, particularly as it would foreclose important connections to country for present and future generations.

I propose that by 2028, as part of the decadal plan, we will have implemented a national mechanism for recording these names for all language groups in Australia, in close and meaningful collaboration with their custodians and the communities for whom they are meaningful. This will be done in ways that are fully cognizant of the potential for cross-cultural miscommunication in any endeavour like this. Importantly, it will be done with due respect for the deep knowledge tradition that’s being recorded, and in a way that’s most appropriate for the needs of communities and of Indigenous people, rather than in ways that are most convenient for us. The prime goal is to record words for the language-speakers, with any advantages to our own community secondary.

 Specifically, this program will not:

  • Send out inexperienced people to record names as a shallow, one-off exercise – this would be disrespectful;
  • Record names in ways and on platforms that are convenient for us but of little use to communities – this would be useless;
  • Be rolled out with minimal consultation from communities themselves – this would not generate trust;
  • Be rolled out as a one-size-fits-all program – this would be ineffective.

 The program could work like this:

  1. A strategic assessment will be made, in collaboration with linguistic and cultural experts, of language groups throughout Australia that still have strong cultural knowledge of plant and animal names, but with the knowledge endangered by imminent loss of cultural custodians and first-language speakers;
  2. In each state or region, one or more skilled, retired botanists be identified and approached, to take part in the program;
  3. After training and with appropriate support, the botanists will build relationships with their counterparts in communities, and seek community views on the need to record names, and the most appropriate ways to do this
  4. During repeat visits, with support from linguists contracted as part of the program, names will be recorded in as simple and straightforward a way as possible
  5. Names will be provided back to communities in whatever format they consider most useful, as well as recorded in national databases to ensure they are safe in the medium to long term.

{Thanks very much to Glenn Whiteman, NT Herbarium, for useful discussions on this idea.}

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tag:notobiotica.posthaven.com,2013:Post/1191075 2017-09-14T01:14:16Z 2017-10-09T22:12:19Z Taxonomy 2028 Challenge: Knowing the origins of the Australian biota

By the year 2028 we will have compiled a database of information on the origin of Australia’s biota. This database will detail the area of origin for every genus within Australia, and the timing of its original arrival in Australia.

Initially, the database could be compiled from published phylogenetic data, eventually being replaced with phylogenetic information which has been analysed in a consistent methodology.  This goal could be achieved through the targeted sampling and molecular sequencing of lineages that have distributions spanning Australia and neighbouring landmasses (Southeast Asia, the Pacific, Antarctica, etc.) and then of lineages with more cosmopolitan distributions. This database will establish an understanding of the unique and varied evolutionary history of the Australian biota, determining which lineages are ancient Gondwanan relicts and more recent immigrants, as well as identifying spatio-temporal patterns of immigration, emigration and diversification in the history of the assembly of the Australian biota. It would also provide an invaluable resource for the advancement of research in Australian biogeography, biogeography theory, invasive species ecology, geology, palaeontology, evolutionary theory, trait evolution and ecology and for informing conservation priorities and strategies.

This phylogenetic information could be integrated into the ALA platform through the addition of interactive phylogenies on each taxon’s ALA page. Clicking on nodes of each phylogeny could show biogeographic, morphological trait and divergence age data for that taxon. Publication of phylogenetic information in such an interactive way would engage the public and raise understanding of the significance of the unique evolutionary histories of groups within the Australian biota. It would provide an alternative visual mechanism for exploring taxa by placing them in a phylogenetic context. It would also provide a platform through which evolutionary concepts are made accessible for lay people, encouraging the the exploration of integrative evolutionary questions and engaging them with concepts in systematics, evolution and taxonomy.

Lizzy Joyce
PhD Candidate - Australian Tropical Herbarium & James Cook University
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tag:notobiotica.posthaven.com,2013:Post/1189861 2017-09-08T23:46:22Z 2017-10-03T09:24:57Z Linneaus and the Ackronyme project (satire)

The following fragment was pieced together from notes written by Jakob Rindler and only recently discovered in a shed at the Liverpool Botanic Garden. It is thought the notes were acquired, together with many other documents and specimens from the Linneaus estate, by Sir James Smith in 1783.

Although not an "apostle" student of Linneaus, Rindler was a summertime house-guest at the Linneaus farm at Hammarby, now a suburb of Uppsala. In the early 1760s a botanic garden was planted at Hammarby, and in several letters from Linneaus, Rindler is mentioned as a young and enthusiastic botanist who was of great help in tending the Hammarby plantings.

Judging from internal evidence, the meeting reported by Rindler probably took place in 1764 or 1765. It is curious that Linneaus never mentioned the interview with Sir Edward Ackronyme in later correspondence.

I have taken the liberty of translating Rindler's notes into reasonably modern English.

***

The master was visited today by an English gentleman, Sir Edward Ackronyme, who carried letters of introduction from Earl Macclesfield [Royal Society of London] and Philip Miller [Chelsea Physic Garden].

The gentleman appeared to be very intelligent and spoke both Swedish and Latin. He praised the master's many contributions to knowledge. He said the master was a scientific colossus of the age and respected by all who knew the master's work. He said famam extendere factis [through our deeds we extend our fame] on the master's coat-of-arms was an inspiration to all natural philosophers.

The gentleman said he had read the second edition of the master's Species Plantarum, and had observed that it was supplemented with corrections to the text and with additional notes. The gentleman had a proposal to make in connection with this.

He proceeded to describe correctly and in interesting detail how Species Plantarum had been written and published, which greatly surprised the master. The gentleman said that his proposal did not, however, concern the production of scholarly books, but instead the use and diffusion of the knowledge in the books.

The gentleman explained that he and others had invented a method for reproducing the master's descriptions, using a large number of scribes and a new means of printing which was very swift and not expensive. The words of the master concerning individual species would be copied out by the scribes and printed in large numbers as separata.

The separata might then be sold more widely than the Species Plantarum. The gentleman gave an example, in which a philosopher in Virginia could acquire the descriptions of plants and animals native to Virginia. The two volumes of Species Plantarum contained many descriptions of plants and animals which were not found in Virginia and might not be of interest to philosophers there. The separata pertaining to Virginia, or to any other place, could be gathered up and placed in a pouch.

The gentleman said that if a purchaser was only interested in Pisces in the master's Systema Naturae, then the separata for Pisces could be gathered together for the purchaser.

The master observed that this was very clever. At this point the gentleman asked the master if the master could see value in this method of diffusion of knowledge. The master replied that it indeed had value.

The gentleman was pleased to hear this, and said that he had also received encouraging replies to this question from other philosophers. The gentleman had spoken directly to Dr Scopoli in Idrija and to other philosophers who had published works of natural history. Each had agreed that there was much merit in the idea of spreading more widely their descriptions and classifications.

The gentleman said that if the master wished to make a correction or addition to any one of his species, that information could be sent to the scribes, who would make the correction or addition in a new separatum. The new separatum would be sent to all those who had purchased an uncorrected version. The gentleman said this was possible because the cost of printing separata by the new method was hardly of consequence, and the number printed could be one or a thousand.

The gentleman produced a small sheet of paper and gave it to the master. On the paper had been printed a description from Species Plantarum of a species, and beneath the description was the name of the master. Beneath the name was an addition the master had made to the description, and this too was subscribed with the name of the master. At the bottom of the paper was a date, which the gentleman said was the date on which the separatum had been printed.

The master again praised the cleverness of the idea of separata. He begged leave to ask questions, and the gentleman agreed.

The master asked first whether there would be a cost to himself in the production of separata. The gentleman said there would be no cost to the master or to other philosophers. The work of the scribes and the printing of separata would have royal patronage. He was not presently permitted to name the royal courts from which the patronage would come.

The master expressed surprise to hear that more than one kingdom was offering to assist. The gentleman explained that the idea of diffusion of knowledge through separata was not his alone. He was one of a group of interested gentlemen distributed throughout Europe. Each member of the group made a particular contribution. His own contribution related to printing, regarding which he could modestly admit to having acquired a degree of expertise.

The group of gentlemen met on occasions in various European cities. Their next meeting would take place in Paris. They would consider the question of whether separata should be printed only in Latin, or also in various modern languages, and if the latter, whether one separatum should be printed in more than one language. The gentleman said there were arguments for and arguments against, and the question might have to be resolved at a later meeting in another city.

Now the master asked, whether the patronage enjoyed by the gentlemen could be extended to natural philosophers and their students. The gentleman apologised because he did not think it possible. The production and distribution of separata was a matter of diffusion of knowledge, not of the generation of knowledge. The gentleman said that he and the other gentlemen greatly appreciated the work done by the master and other natural philosophers. It was the humble role of the gentleman and his associates to spread that knowledge and to make it more useful.

At this the master became upset and spoke severely. He said he worked day and night on the investigation of a science that a thousand men will not be able to complete, to say nothing of the time he squandered every day on scientific correspondence, while the gentleman and his colleagues can constantly enjoy the amenities of life. The master said that separata may indeed be of value, but they add nothing at all to knowledge, and that the gaining of knowledge was his constant goal.

The gentleman said that he hoped nothing he had said had angered the master, and that he had one more question to ask. While the scribes were skilled and diligent, it occasionally happened that a copying error was made when producing the separata. The gentleman asked whether the master would be willing to examine drafts of separata before they were printed. He explained that he and his associates were not natural philosophers, and that natural philosophers would be the persons best able to locate and correct any errors.

This concluded the meeting with the gentleman. The master did not reply to the last question, but wished the gentleman a good day, and turned to me and said that there was work to be done in the garden.

- Bob Mesibov


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Bob Mesibov
tag:notobiotica.posthaven.com,2013:Post/1189366 2017-09-08T22:20:52Z 2017-10-13T06:08:46Z A Dream of Invertebrate Utopia

I am continually impressed by the diversity of views and proposals for the Decadal Plan coming from different parts of the taxonomic community in Australia.  The project has brought some quite disparate communities together to discuss common goals as they have never done before.  

More and more I see the broader taxonomic community divided into two camps, those that are working on less diverse and relatively well-resourced taxonomic groups, and those that are working on very diverse but relatively poorly resourced groups.  Taxonomic groups don't switch between these camps, it is destiny, so resourcing differences become magnified and accentuated over generations and centuries.  

There has now be come such a huge divide between the "haves" and the "have-nots" that it has become a challenge in and of itself.  Much as rising income disparity is now seen as a major challenge for western democracies.  The differences between the "haves" and "have nots" are now so profound that priorities and solutions are often different depending on the camp the particular idea originated in.  I think it is also important to acknowledge the illogical, emotionally-driven and innately human process by which taxonomic groups end up in the "have" or "have not" category.  You could logically conclude that resources available to western science for taxonomy have only ever really scaled to the small groups of obvious macroscopic organisms, such as vertebrates and others, together representing just 5% or so of species.

The large and random differences in our taxonomic knowledge of different groups has a negative impact on biology generally.  It hampers any study that attempts to examine communities or ecosystems from a process or systems perspective.  We know some macroscopic species well, but are ignorant of species to which they are intimately connected and critically dependent, simply because those connected species happen to belong to one or more "have not" taxonomic groups.  

I wrote this little satirical piece of whimsy that imagined one of the "have not" groups, the weevils (Curculionoidea: Coleoptera), historically had been included as one of the "have" groups.  Hopefully it will cast some light on the different resource levels available to the "haves" and "have nots". I think we need to fully appreciate the challenges these institutional and resourcing differences have stamped on our communities before we can move forward together.

 

A Dream of Invertebrate Utopia

With satirical apologies to George Orwell’s Animal Farm

 

I don’t know how it all started, perhaps back in the 1700’s naturalists imagined that there were as many weevils as all other animals and plants, but that is not really my concern.  Quibble with the numbers, we now estimate that there are around 20,000-25,000 weevil species here, and they make up about 5% of Australia’s biota, in other words we have about as many weevil species as butterflies and moths, or plants. As we intensify our focus, we are discovering more and more new Australian weevil species.

Our scientific community studies weevils (Curculionoidea) because they are extremely diverse and occur all over Australia.  They are ecologically important, some species are pests, others are biosecurity threats and yet more are biological control agents.  You can walk into any Australian environment from the wet rainforests to the arid inland, and find a unique community of weevils.  Weevils first appear in the fossil record 160 million years ago, and Australia is home to some of the early branching lineages.  Our weevil fauna includes giant Eurhamphus that feed exclusively on southern hemisphere pines. Weevils are some of the most damaging pest of timber and stored grain, so understanding weevils is vitally important for our economy. Besides that, they are cool! 

Right back at the beginnings of the development of each state, and in the commonwealth, we set up large institutions devoted to the study of weevils, called Weevilariums.  These institutions are going strong today each with 20-30 paid staff beavering away studying the taxonomy, biogeography and phylogeny of Australia’s weevils.  And the good news is we are getting ever so close to finishing the job!

Each state Weevilarium has worked hard over more than a century on the taxonomy of the weevils from their state.  You really can gather some momentum with that sort of workforce over that many generations.  First we produced hard copy book series called Weevils of NSW, etc.  Turns out that we worked so hard in each state we had described many species more than once - especially those that cross state boundaries.  But that doesn’t matter-why just deliver when you can overdeliver, I say!  Now we are putting all the weevil treatments together electronically with commonwealth funding, and we really are going to have to sort out those overlaps once and for all.  Kind of a victory lap. Thank goodness for forward planning!

The Australian Weevilariums are incredibly well connected globally, and we even have set up a bespoke international code of nomenclature just for weevils!  Nothing like a specialist tool for a specialized job.  Now the codes for weevils and the remaining biota have diverged quite a bit, like Spanish and Portugese.  Sometimes if you know one you can read bits of the other, but if people are talking nomenclature the two systems are incoherent!

Thanks to commonwealth weevil digitization funds, we now have almost all 10 million weevil specimens in the Weevilariums databased, we have developed great lists of all the weevil species in each state.  We are making great headway in imaging all weevil type specimens.  We can now map and model weevil distributions with great accuracy, and search for areas of endemism and high species diversity with great sophistication.  We have very detailed information on weevil abundance, and have listed many species as rare and threatened with the appropriate authorities.  Weevil conservation biology is now an expanding field, generating large amounts of external income for the community. We even had a Weevil Liason Officer position at the Natural History Museum in London for more than 50 years sorting out the curly issues to do with weevil type specimens in European museums.

We now have a great self-sustaining system with academics at universities studying weevil taxonomy, teaching courses in weevil taxonomy and biology, churning out PhD graduates that can take positions at the Weevilariums. Our Australian Systematic Weevil Society meetings are attended by more than one hundred engaged professionals and students each year. We even have our own special weevil subcommittee to assess and recommend commonwealth funds for weevil taxonomy.  Nothing like having real experts making the big decisions! Probably something like 40% of the resources available for taxonomy in Australia are now devoted to weevils. 

Weevil larvae eat plants, but we are so busy studying weevils that we rarely take samples of the plants they are feeding on.  Early on in my career I took a few samples to the grumpy old retired guy who passes for our Australian plant taxonomy expert.  I had to keep badgering him for the ID’s, and after a few months he said none of the plants were described anyway.  Bit of a waste of time, but I did at least give him a chance!

We even have a number of weevil egg banks dotted around the country.  Weevil eggs are in demand because they are used in biological control programs both here and overseas.  In Canberra we have an egg bank for small weevils, a separate egg bank for big weevils, and there is another one for weevil eggs of all sizes just outside of Sydney.  We are planning brand new facilities for the two Canberra egg banks.  You can’t have enough new weevil egg banks, I say!

Looking back over the field it is clear that the high level of investment in weevil taxonomy has given us a huge head start in comparison to the taxonomic knowledge of almost every other group.  I suppose we really could learn more about weevils place in ecosystems if we knew a little more about the plants they feed on, for example.  It would also help with their conservation as well.  I guess weevils are really a boutique slice (5%) of our biodiversity. But what a great example we have provided for the communities studying other taxonomic groups to follow!

Our real focus these days is the tiny (0.5-1.0 mm long) black and brown weevils.  I don’t know what we will do once we have finished the taxonomy of Australia’s weevils.  Maybe move on to the Cerambycidae (longicorn beetles), another hugely diverse, ecologically important, related group.  But there is a lot to be said for just sticking to weevils.  With grand institutions to fill, new technologies and theories to apply, we may never finish!

   

Then I woke up, and reality dawned on me.  There are no Weevilariums in Australia or the world.  There is one professional weevil taxonomist working here on our fauna of 20,000-25,000 species.  Our weevil taxonomist is entirely supported in the Australian National Insect Collection by a generous bequest of millions of dollars from a philanthropist.  Without this gift there would be precisely no weevil taxonomists in Australia. Our weevil taxonomist is expected to revise a large chunk of the Australian weevil fauna during his career, as well as provide continuing advice in biosecurity and pest management.

With this level of investment we will never know the weevil fauna of Australia in any coherent time frame, and we invest even less in the study of almost every other comparably-sized invertebrate group.  I have chosen weevils as the subject of this satirical piece for convenience, any number of other comparable invertebrate groups could substitute.
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tag:notobiotica.posthaven.com,2013:Post/1188937 2017-09-05T11:55:45Z 2017-10-10T06:00:07Z Counting species - questions and meta-questions

Yet another paper has come out (Larsen et al. "Inordinate fondness multiplied and redistributed: The number of species on earth and a new pie of life" The Quarterly Review of Biology 92(3): 229-265, 2017) asking the perennial "how many species are there on earth" question.

This is potentially an important question, and potentially a non-question. The question (whether it's important or not a question) is in turn important for the decadal plan, but also more broadly for biology as a whole. I'll return to the decadal plan later.

This issue is a problem, because current estimates for the number of species on earth vary from ~2 million (see refs in paper above) to ~1 trillion (I don't even really know how big a trillion is, but it's much bigger than 2 million). The paper above takes a stab in the dark (the authors would dispute this) and puts the figure at 1–6 billion. 

Take your pick. That's our problem. The number can be almost anything you want it to be.

But I think there's a bigger problem, which is that none of the studies that make these estimates ask what I think is the most important question, which is: does the how-many-species question make any sense? (Or more precisely, is the question answerable? The studies assume that it is, without justifying this assumption.) 

This is a meta-question, a question about a question. Until we can answer the meta-question, trying to answer the question is almost certainly futile. Let me explain; but first, let me digress to the late 18th Century.

At that time, some of the most influential French scientists (Jussieu, Adanson, De Candolle) had an important argument about the "shape" of nature. Jussieu (one of the leading scientists in the post-Linnaean world) argued from first principles that nature was continuous. He believed that somewhere out there (and increasingly being discovered during the great age of exploration) existed an intermediate form between every recognised taxon. There would be found organisms that would bridge the apparent gap between all species, between all genera, all families, all orders etc. Nature, in Jussieu's view, would prove to be a complete continuum, and taxonomy would eventually become an utterly arbitrary division of that continuum, just as colour terms arbitrarily divide the spectrum of visible light. Jussieu, by the way, was perfectly comfortable with this.

Adanson and De Candolle, by contrast, believed that the gaps observed between clusters of closely similar organisms were real, and that a relatively non-arbitrary ("natural") taxonomy could be based on the identification of these gaps. What's more, they believed that the cluster-and-gaps pattern could be discerned at all taxonomic levels, allowing us to create a natural classification of species, genera, families etc.

Adanson and De Candolle won. Nature was found to be inherently gappy; they had invented a (non-algorithmic) form of the phenetic method; and a century-and-a-half of a "taxonomy of the gaps" ensued.

Phylogenetics has slightly changed our views on all this, but only slightly. We're now interested in clades and all that, of course, but (at least at species level) we're still very keen on gaps. We now use terms like coalescence; the issue may take the form of working out what percentage difference between two barcodes is required to infer two species; it's still about gaps.

But - what if Jussieu was right? Not exactly right in the sense that there is a continuum of forms, but right in the sense that there's a continuum of gaps. What if there are big gaps (between e.g. a tuatara and its nearest relatives) down to small gaps (between two closely realted species) to smaller gaps (perhaps between "cryptic species") to very small gaps (the ones that the next generation of taxonomic splitters may use to ensure that taxonomy is a never-ending science, and that some orchid taxonomists use today - sorry, couldn't resist the dig). 

What does this mean to our question "how many species are there"? It may mean that the answer is whatever number you want it to be. Curiously, that seems to be about where we're at.

The problem can be rephrased in modern terms: is the pattern of variation in nature (call it its shape) fractal? A fractal pattern would be one where the pattern of "gappiness" is about the same all the way down. The gaps become finer and finer, but we can discern gaps all the way. If nature is fractal in this sense, then asking the question "how many species are there" is as meaningless as the classic fractal example "how long is the coastline of Australia?" There's no answer to that question. If you measure Australia's coastline on a 1:1,000,000 map you'll come up with one estimate; if you trace around every headland and minor prominence you'll get a much larger answer; if you trace around every grain of sand on every beach you'll get a larger answer still. In a fractal system, some questions are silly.

If, however, the shape of nature is non-fractal and there's a minimum observable gap, which we could use to objectively delimit species, then the question isn't silly at all (it's merely difficult).

So - I think we need to answer the meta-question ("Is the pattern of variation in nature such that the question of how many species exist is answerable?") before we try to answer the question ("how many species exist?"). An important question is - how could we go about answering the meta-question?

A thought experiment may help. Imagine that we had a full genome sequence of every individual organism on earth (no, I'm not suggesting this as a goal for the decadal plan). We could then use a super-super-computer to calculate the pairwise distances of every individual from every other individual, and plot these on a graph (increasing distance on the x-axis, frequency of that distance value on the y-axis). There would be a wide spread of pairwide distances on our plot, from close to zero to some arbitrarily large number. 

If the shape of nature is fractal, we'd see a complete spread of distance values with only random troughs and peaks; if, however, there's a real "species-gap", we'd see a distinct, non-random dip in the frequency distribution at some distance value somewhere closeish to the x-origin.

Our dataset would allow more sophisticated analyses. We could partition the data into different taxonomic groups (do we see a species-gap in, say, spiders as well as in bacteria, birds and plants - and importantly, if we do is it in the same place?). We could also partition into different ecological niches (do rainforest taxa have a gap in the same place as arid-zone taxa?; do r-strategists have a gap in the same place as K-strategists?), or breeding systems (do taxa that use sexual selection have a gap in the same place as taxa that don't?).

When you think about it, a graph like this would give us crucial insights, not only into the meta-question discussed here, but to help assess utility of e.g. barcodes for species delimitation. 

For what it's worth, my own guess is that we wouldn't see a magic value on a graph like this, but rather a random pattern of peaks and troughs all the way down. That is, my guess is that the question "how many species are there?" is a silly question.

Of course, like all good thought experiments, we could never do this. So this opens a new question - can we approximate the graph using real-world data sets? One possibility may be to use environmental genomic data - this has the advantage that it's presumably sampling sequences from every individual in the genomic soup, with no inherent taxonomic bias or pre-assumed taxonomy. I have no idea whether this idea has merit, and would be pleased to hear from someone who actually knows what they're talking about in this space.

One final question - do we try to deal with this issue in the decadal plan? We need to be careful about admitting that we have absolutely no idea how many species are in Australia and any estimate could be out by many orders of magnitude (this is not a great starting point for asking for funding to document our biodiversity). But we could argue for a project that addresses the meta-question, if indeed there's a way to address it. Now that would be a world scoop, I reckon.

As always, thoughts and comments very welcome.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1188640 2017-09-04T02:09:35Z 2017-09-05T00:07:09Z Roger Shivas

I am a mycologist and plant pathologist. My research interests are the systematics of fungi, especially those that cause diseases of plants and insects.

Currently I have two jobs, one as curator of the Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries as well as a professor (mycology) at the University of Southern Queensland.

Further information about the work that my colleagues and I do can be found at http://collections.daff.qld.gov.au

Dr Roger Shivas

Principal Plant Pathologist
Biosecurity Queensland
Department of Agriculture and Fisheries
GPO Box 267, Brisbane, Qld 4001

Tel. 61 7 3708 8478
Email: roger.shivas@daf.qld.gov.au

 

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tag:notobiotica.posthaven.com,2013:Post/1188225 2017-09-02T02:50:48Z 2017-10-13T01:39:38Z What about the passionate?

You've probably noticed: taxonomists aren't quite like other scientists.

They have a powerful fascination, if not an embarrassingly strong affection, for "their" groups of organisms. As the TV professionals say, they're great talent, because they talk excitedly on camera about their favourite taxa.

They study particular taxa for decades, becoming the experts — the "names" — to whom the biosecurity and agriculture sectors turn for advice.

They get better at what they do as time goes on. Taxonomists hit their stride in late career, peaking in their 50s and 60s and often publishing valuable papers in their 70s and 80s.

They can be relatively cheap to run. Unless they're focused on molecular systematics, the annual costs for their taxonomic work might amount to just a few thousand dollars.

They don't require a lot of formal training. Some of Australia's best taxonomists are self-taught in their specialty.

They can communicate with the public directly about ideas the public already understands: "species", "discovery", "natural habitats", "invasive organisms". Only rarely do taxonomists need a professional science writer to background and explain what they've done.

Granted all this, previous calls for more public support for taxonomy in Australia seem a bit misdirected.

There's the call for more training money in Australia's universities, which gave up teaching taxonomy long ago. Instead the universities turn out PhDs with only the dimmest understanding of the maths behind the sophisticated phylogeny-guessing software they've relied on, and a similarly limited understanding of their study taxon's biology. The door opens, the new PhDs leave and compete with all the other science PhDs for work, leaving behind an interest in the taxa that helped them get a degree.

There's the call for increased infrastructure spending on museums and herbaria, which is great, because taxonomists depend on collections. But if an increased collections spend isn't paralleled by increased taxonomic work in those collections, what's the point? Without more curators and supported visitors, museum managers are justified in asking "Why do you need more than one specimen of each species?" and "How is any of this bringing more people through our doors?"

There's the call for more IT spending to aggregate more collection and other species-tied data, and to put those data at the fingertips of... umm, somebody... with a browser. Who will then spend days cleaning the downloaded data because the IT funding included not one brass razoo for data cleaning at source (disclaimer: I'm a data auditor as well as a taxonomist).

What's missing from these calls? Any mention of the people we need more of, those passionate taxonomists.

Here are four ways those people could be encouraged and supported:

(1) Find them and train them: "We're looking for people who are absolutely fascinated with particular Australian life-forms, and we'll back your passion with taxonomic training. You may not get a career out of this, but we'll give you the tools for a lifetime of satisfying study and of contributions to knowledge of the Australian biota."

(2) Get the collections to reach out. Ensure that museums and herbaria have enough money to host taxonomist volunteers, and to sponsor short-term visits by specialists, including non-professionals.

(3) Reward productive taxonomic work. How about ABRS offering up to 50 $5000 annual grants per annum (up to $250 000 total) to currently publishing taxonomists, renewed every year? The money could be used for collection visits, field work, publishing fees, conference attendance and project-tied costs such as sequencing and SEM work. Unaffiliated and retired specialists would welcome even this small drip-feeding of taxonomic support. The risk per grant (the risk that the money is wasted) is trivial and easily minimised by cancelling payment if there's no evidence that productive taxonomic work was done in the preceding year.

(4) Pay for mentoring. There aren't any succession plans in Australian taxonomy, despite the fact that for every specialist there are dozens of non-specialists with an existing or potential interest in working with what could otherwise become an orphan group. We know those potential mentorees exist: the BowerBird project has brought hundreds of keen non-professionals out of the woodwork. Why not directly support the transfer of specialist knowledge, with travel grants for joint collection visits and field trips?

OK, it's obvious. I don't see taxonomy fitting entirely within an academic framework, which is how many taxonomy promoters want governments and other funding sources to see it. Instead I see taxonomy distributed widely within the Australian community, with weekend, holiday and retired collectors and enthusiasts being part of a broad collaborative effort. That's probably because I'm goal-focused. I want to see increased taxonomic effort in Australia, and that's not the same as an increased number of professional taxonomists.

- Bob Mesibov
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Bob Mesibov
tag:notobiotica.posthaven.com,2013:Post/1188223 2017-09-02T02:41:01Z 2017-09-04T00:27:41Z Bob Mesibov

Bob Mesibov

I'm retired and I study millipedes.

Since 2002 (just before I retired) I've described or redescribed about 200 Australian millipede species. My Millipedes of Australia website is a resource for taxonomists and offers more than 14000 vetted locality records for named species as downloadable TSVs and KMLs.

In 43 years of collecting in Australia I've visited ca 3200 unique localities and deposited thousands of millipede specimens in museums in New South Wales, Queensland, Tasmania and Victoria.

I'm also a coder and data auditor, and spend a lot of my time happily working on the Linux command line.

For more about me and my Web resources, please visit polydesmida.info.


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Bob Mesibov
tag:notobiotica.posthaven.com,2013:Post/1187953 2017-09-01T04:03:16Z 2017-09-01T04:03:16Z Taxonomy 2028 Challenge: 75% of species of Australian arthropods described by 2028

Posted on behalf of Penelope Mills, PhD candidate at The University of Queensland, working on the systematics and evolution of two groups of gall-inducing scale insects of Apiomorpha (Hemiptera: Eriococcidae).


By 2028 we will have described ~75% of species of Australian arthropods.

Arguably, phylum Arthropoda contains some of the most important species on the planet. They are also the most numerous group, and include about 80% of all the described species. However, much of the biodiversity within arthropods remain undescribed. Even within this current age of genomics, much of the research concerning Arthropoda focusses on a narrow breadth of species (e.g. medically-important species, agricultural pests, species of quarantine concern).

Many biodiversity surveys and estimates use species as the unit of measure. This means that better-known groups (e.g. chordates, angiosperms) are commonly included in biodiversity estimates, whereas the most numerous groups (e.g. Arthropoda) tend to be ignored because most species are yet to be described or can not be identified to species level.

There are already systematic grants available from ABRS and BushBlitz to nurture the discovery and documentation of Australia’s biodiversity. However, additional funding from government agencies, including the ARC, should be sought for funding basic taxonomic research to increase the achievability of the proposed goal.

The difficulty will be in convincing the funding panels and the public that this research is necessary and has far-reaching implications. Putting a name to a species allows it to be considered for biodiversity and conservation purposes, and the additional data provided by the description can be used by multiple digital platforms currently in place (e.g. Atlas of Living Australia, BowerBird) to examine additional questions about Australia’s biodiversity.


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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1187693 2017-08-31T02:09:26Z 2017-08-31T02:11:36Z Taxonomy 2028 Challenge: Using citizen surveillance applications to increase the number and frequency of culture collection samples for genomic analysis.

Posted on behalf of Andrew Taylor, PhD candidate Murdoch University and Research Officer DPIRD WA (andrew.taylor@dpird.wa.gov.au)


By 2028 genome sequencing will be common place amongst laboratories as technology improves and costs fall. This will result in more organisms having their genome sequenced and will lead to the taxonomic re-evaluation of a number of economically important plant pathogens. The oomycetes are one group of plant pathogens that are economically important to a diverse number of horticultural commodities and amongst natural ecosystems. In many instances they are also known to develop fungicide resistance rapidly, making control problematic. It appears from the number of oomycetes that have had their genome sequenced a taxonomic re-evaluation is likely.  

A characteristic of a number of oomycetes is that they are obligate biotrophs, meaning they can only be stored in culture collections on samples of the infected host. Often only a few of these representative samples exist and the collection dates are sporadic, in many cases multiple decades apart. This creates issues for researchers as it means samples lodged in collections are not allowed to be released as DNA extractions are considered destructive sampling. It also creates issues with biosecurity policy. With the likely taxonomic changes as a result of genome sequencing it will be difficult to gain access to old samples to be able to update prohibited organisms under re-evaluated classifications.

The proposal I put forward is to use the development of citizen surveillance applications that are being developed for a number of horticultural commodities across Australia to place call outs for samples of oomycete plant pathogens on a regular basis so that a greater number of culture collection samples can be submitted. A regular basis could be every 5 years or based on all diseases of a specific commodity using a similar timeline. Sample bags can be sent to responders with specific instructions to optimise collection and storage quality. Approaching the rural levy provider to fund the sampling and provide advertising would assist in costs associated with the sampling. 

The benefits of this proposal:

  • Provide enough samples in the collections to allow for DNA extractions without restrictions or as the technology improves.
  • Population data on a number of economically important plant diseases. This could be further used for:
    • Surveillance data for biosecurity purposes (includes nil results).
    • Genotypic information for fungicide resistance projects.
    • Information on the lineage of the disease over time, is it moving to more aggressive strains?
  • Allow citizens and industry to be included and feel invested in potential scientific research.
  • Cost effective way of collecting samples over a wide geographic area.
  • Cost effective for the levy providers as it would allow for long term collections rather than the boom and bust cycle of funding large scale projects. Often after large scale projects are completed the samples are destroyed meaning new projects spend money on recollecting samples.  
  • Provide information as to disease hot spots or location of prevalence over time.

This proposal could be broadened to a wider group of pathogens but I have written it from the basis of my PhD experience with oomycetes.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1187186 2017-08-29T01:40:56Z 2017-08-30T00:17:23Z Taxonomy 2028 Challenge: We need to database all specimens in the national collection, focusing on museum collections

When the Australasian Virtual Herbarium (AVH) was initiated in 1999, herbaria had for many years been databasing specimens. The AVH was seen as a logical progression from isolated specimen databases in each institution to an aggregated, national database of all specimens. Funding, obtained on the basis that the AVH would stimulate research including taxonomy, was obtained and used to complete the databasing of Australian specimens in all major herbaria, to mount and database backlog specimens, and to develop the AVH infrastructure.

Museums and other zoology (e.g. entomology) collections have also been databasing specimens for many decades. However, no museum collection is fully databased. OZCAM, the museum equivalent of AVH, is also an aggregation service, but museum collections have not had the benefit of a large, national, coordinated, funded campaign to database all specimens. This is a severe constraint on biodiversity inventory, mapping, biogeographic and ecological analyses in Australia.

By 2028 we will have databased half of all specimens in museum and other zoology collections, with a sustainable program to database all specimens within the following decade

Databasing museum and other zoology collections is a substantially bigger task than databasing all herbarium collections. The AVH includes >8 million records, comprising c. 80% of the estimated number of plant, algae and fungi specimens in Australian and New Zealand herbaria. OZCAM includes <4 million Australian records, comprising c. 6% of the estimated total number of specimens in Australian zoological collections. The task is large.

However, the benefits are also very large. The fact that the vast majority of zoological specimens are un-databased precludes us from doing simple tasks like drawing accurate distribution maps for most taxa, assessing the conservation status of taxa, determining where rare taxa occur and whether they occur in sites targeted for development such as mining or agricultural clearing. The AVH is now used by researchers all around the world for novel biodiversity analyses in areas ranging from evolution, ecology, biogeography and conservation, and has amply proven its value. A completed OZCAM would be even more valuable.

We now need to work out a way to invest the necessary effort into our zoological collections.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1187178 2017-08-29T00:31:45Z 2017-08-29T00:33:11Z Taxonomy 2028 Challenge: The view from an obligately biotrophic fungus

Posted on behalf of Professor Levente Kiss, Centre for Crop Health, Institute for Agriculture and the Environment, University of Southern Queensland

Prof. Kiss writes: As a newcomer in the Australian scientific community (I started to work here this year), I am deeply impressed by, and highly value, the Decadal initiative. During the past >25 years, I have been mainly interested in the biology, and taxonomy, of obligate biotrophic fungi, so I’ll focus on this group below.


We’d like you to scan the horizon, and share what you see.

It is an ‘easy’ assumption that during the next years more and more DNA loci will be used for taxonomic purposes. In fungal taxonomy, these new, or already exploited loci may not be useful for the whole Kingdom, and could be lineage-specific, as already shown in some cases by Schoch et al. (2012). (If interested, see my commentary about this paper: Kiss 2012). By the way, the identification of phylogenetically / taxonomically relevant lineage-specific DNA markers could be a general trend in future taxonomic works, within each Kingdom. Also, it is likely that whole genome analyses will be more widely used in taxonomic works, although this approach will always be limited by availability of funds, no matter how inexpensive will sequencing become, and methodology constrains, as well.

One aspect, which, in my opinion, has sometimes been forgotten, or at least neglected, especially in fungal (and, more generally, in microbial) ‘phylogeny only’ taxonomic works, is that, after all, different taxa have to be recognized as entities held together through gene flow. In obligate biotrophic fungi, where neither growth nor asexual and sexual reproduction are possible without being structurally and nutritionally linked to the living host tissues, gene flow cannot be envisaged if the respective fungi do not share the same hosts. However, in some groups of such strictly host-associated fungi, current practice is to apply the same taxon name for organisms that are unable to meet, and recombine, in/on the same hosts due to their narrow host specializations, but share identical, or highly similar, DNA barcode sequences. It has long been highlighted that gene phylogenies should not regarded as species phylogenies (Doyle 1992); however, the DNA barcode approach, as a quick-and-dirty method, has often been used in describing, for example, strictly host-associated taxa without taking in consideration obvious constraints in gene flow.

Where would you like taxonomy and systematics to be in a decade?

In obligate biotrophic fungi, when it comes to the future of taxonomy, my prediction is that their experimentally revealed host range, and, thus, the detection of whether gene flow is at all possible within a newly recognized taxon, will be much more considered during species descriptions, and will become a basic requirement in this process, in addition to developing better phylogenies for different taxa. Personally, I don’t think this approach can be skipped by whole genome analyses, as host specificity may be determined by a very small fraction of the genome, which may remain unrevealed when performing analyses of huge datasets.

What achievements or programs would you like to see in place? What milestones would you like us to pass?

I assume sequencing coupled with new DNA barcode developments, with direct taxonomic implications, will continue, and will always be fueled by the biotech sector. Specific taxonomic and/or biodiversity programmes (such as many more ABRS projects) focusing on those groups of organisms (in our case: fungi), which are challenging from a methodological point of view, and require specific approaches, in addition to the sequencing work, would lead to real breakthroughs in this field.

What innovations in technology, infrastructure, funding or organisation will make a big difference to your work and to our taxonomy and systematics?

I’d focus on the taxonomy of those groups of organisms (fungi) which are difficult to handle, due to their specific way of life (e.g., obligate biotrophs vs. free-living fungi). In taxonomy, personal expertise, special skills, are usually much more important than special infrastructure, therefore funding schemes should focus on key scientists and their students (i.e., salaries, fellowships), and should provide long-term support. In the USA, the NSF PEET scheme seems to be a great initiative to support taxonomic research, and especially training a new generation of taxonomists:

https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5451

References

Doyle JJ (1992) Gene trees and species trees: Molecular systematics as one-character taxonomy. Syst. Bot. 17: 144-163.

Kiss L (2012) Limits of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences as species barcodes for Fungi. Proc Natl Acad Sci USA 109: E1811.

Schoch CL, et al. (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA 109: 6241-6246.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1186422 2017-08-25T07:14:50Z 2017-08-25T07:14:50Z The Taxonomy 2028 Challenge: Validation of Australia’s vascular plant collection data

Herbarium collections are the primary source of verifiable data on Australia’s flora. The information associated with each collection — including the taxon name and its locality — underpins research across a broad range of disciplines. Thanks to advances in cyber-infrastructures and the development of novel bioinformatics tools and techniques, biodiversity and distribution data can now be explored and analysed within a phylogenetic and environmental framework, providing a greater evolutionary understanding of our flora and novel data to inform conservation planning. However, to maximise the outcomes of big data analyses it is imperative that we improve the quality of the data upon which these analyses are based.

Specimen identification errors are commonplace in herbaria and are not confined to taxonomic groups that lack a recent monograph — they also exist (to varying degrees) in groups that have been revised in the past 40 years, most notably in collections that have been made subsequent to a taxonomic treatment or have otherwise not been examined by the treatment’s author. Geocode errors (e.g. mistakes made at the point of data entry, miscalculations and labelling errors) are similarly rife, and can be extreme to relatively minor in magnitude.

Taxonomic and geographic errors in our biodiversity data reduce our knowledge of a taxon’s distribution and habitat requirements, result in the dissemination of inaccurate information to our stakeholders (e.g. incorrect distribution maps, wrongly identified voucher specimens and photographs), undermine the results and interpretation of phylogenetic studies and the accuracy of spatial analyses or environmental modelling, and may significantly impact conservation planning at the species or regional level. Furthermore, a significant amount of useful, high quality data remains inaccessible in specimen backlogs.

By 2028 all vascular plant collections in Australian Herbaria will be audited for taxonomic and geographic accuracy

The audit should include: a taxonomic assessment of all collections, with an emphasis on those that have not been verified by a taxonomic expert; cross-checking duplicates of a single gathering housed at different herbaria to ensure that they have matching identifications (and are therefore represented by just one dot on Australasia’s Virtual Herbarium); preparation, database and taxonomic verification of all backlog materials, including undatabased collections that are currently on loan to other institutions; and validation of locality and geocode information, particularly for all geographical outliers that have been taxonomically confirmed. It would be possible to value-add to this process by capturing information on the reproductive state of every specimen (i.e. whether flowering, fruiting or sterile) thereby informing future collection needs and phenological research.

An audit would lead to the discovery of new taxa and new populations of conservation-listed taxa. Indeed, many scientists are undoubtedly already aware of new taxa that are represented in herbarium collections but are not yet on the National Species List — this knowledge should be captured as part of this process, particularly if taxonomic publications are unlikely to be forthcoming in the short-term. 

An audit would improve the quality of data fundamental to our understanding of Australia’s biodiversity and its evolution. It would underpin the eFlora of Australia, enabling more accurate descriptions and distribution maps to be generated, and would improve the quality of derivative products such as regional or taxon specific Apps and field guides. An audit would have tangible conservation outcomes, providing better information for individual taxa and improving analyses directed at conservation planning and decision making, and would also reduce the amount of time required for data cleaning prior to a large-scale analysis.

Identification errors often arise from imperfect taxonomic knowledge and as such an audit of this nature could not be completely uncoupled from baseline taxonomic research; however, it would focus attention on future research needs (e.g. specimens, species or groups in need of further research could be flagged and prioritised; potential student research projects could be highlighted) and collection gaps.

We will need a significant number of skilled research scientists and identification botanists to conduct a taxonomic audit of collections at their home institution, collections originating from their home state but housed at other national herbaria, and specimens belonging to their taxonomic speciality groups. We will also need additional curatorial staff to database backlog material, validate questionable geocodes and localities, perform database edits and maintain existing collections (e.g. duplicates from other states). Staffing levels will need to be maintained into the future to ensure incoming collections are processed and verified without major delay.

Our collections underpin everything — let’s give them the attention they deserve.




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Juliet Wege
tag:notobiotica.posthaven.com,2013:Post/1186405 2017-08-25T04:37:33Z 2017-08-25T04:38:45Z Taxonomy 2028 Challenge: Collection and characterisation of parasites and symbionts alongside their hosts

Posted on behalf of Dan Huston - PhD Candidate, School of Biological Sciences, The University of Queensland


Organisms do not exist in isolation. Rather they exist in a web of complex associations with other organisms across space and time. Parasites and other symbionts are intimately associated with their host organisms and represent a massive component of global biodiversity. This component is mostly unseen, and rarely considered during biodiversity and ecological surveys or in conservation planning. Threats to biodiversity are amplified in parasite and symbiont populations, and host-specific lineages are likely to face extinction before their hosts. If we seek to characterise all of Earth’s biodiversity then, we must consider symbionts. Obviously, study of these organisms requires examination of their hosts, and therefore presents excellent collaborative opportunities for systematic biologists working on various groups. However, most parasites and symbionts have specific collection protocols required for producing specimens of a quality useful for taxonomy. Therefore I propose that:

By 2028, we will have established and implemented a collaborative support network dedicated to the collection and characterisation of parasites and symbionts, alongside characterisation of their hosts.

It could be called something that would result in a hip acronym like ‘Systematics of Symbionts and Parasites Support Network’ (SSAPSN). The major goal of the network would be to facilitate parallel host and symbiont collection efforts through coordinated collecting expeditions and training about parasite and other symbiont collection techniques. This will result in more impact per unit of collecting effort and more complete biodiversity collections in museums and other institutions for current and future research. Collaborative efforts between those systematic biologists studying hosts, and those studying the symbionts of said hosts may be seen as a better value for money and could increase grant application success, and may lead to cross-field citations of research papers. Most importantly, such efforts will give us a better understanding of life and the complex interactions between organisms in general.

Examples of the importance of considering parasites and symbionts in the future of taxonomy and systematics can be gleaned from many of the challenges already posted here on Noto | Biotica. Elaine Davidson’s challenge to explore the diversity and potential of microorganisms highlights the value these organism have to humans in terms of medicine, agriculture and industry. The many endosymbiotic microorganisms present in plants and animals are sure to provide novel chemical processes and enzymes of value to us. Kevin Thiele’s posts ‘every Australasian species genomed’ and ‘life in the late Anthropocene’ challenge us to collect tissue samples for all Australasian biota and sequence their genomes. While many of the tissue samples required are already in museums, such an endeavour will still require a huge collecting effort. These collecting events should be coordinated between systematic biologists across disciplines so that both host tissue and symbiont tissues can be collected concurrently. Nerida Wilson challenged us to double the number of described coral reef taxa by 2028. This topic hits close to home as much of my PhD research has been on coral reef parasites. We have only just begun to scratch the surface in terms of understanding parasite and symbiont diversity on the Great Barrier Reef and increased effort in characterising these organisms will greatly aid in doubling the number of described species for the region. Juliet Wege’s post ‘Obtain high quality collections of all undescribed vascular plant taxa’ highlights the difficulties inherent in acquiring these specimens from remote areas, and the need to execute targeted field expeditions to take advantage of seasonal weather conditions. Expeditions for rare plants could benefit from a nematologist to collect and study plant-parasitic nematodes and an entomologist to collect and study associated insects. A simple alternative would be training in the collection of these organisms for the botanists tasked with undertaking such expeditions. I fully understand that having collectors plan on collecting symbiont organisms alongside the stuff they are really interested in is a big ask, so including extra personnel on such expeditions focused on symbionts would be ideal. In the end however, any collection would be better than none.

The obvious first step towards building such a network is a level of organisation and a platform for communication. The existence of the SASB and now Noto | Biotica already gets us most of the way there. Noto | Biotica could be used as a news platform to help connect parasite and symbiont systematic biologists with those studying other groups, coordinate collection events, ‘wanted organism’ ads, etc. Because many parasites and symbionts are hidden in not so obvious locations in their hosts, and many require specialised fixation and preservation, workshops designed to train other systematic biologists in how to find these organisms and how to preserve them would be beneficial. Perhaps some small grants could become available for biologists undertaking collecting expeditions to cover the cost of extra field days and equipment to collect symbionts, or perhaps travel grants could be used to bring a parasitologist (we make for interesting dinner conversation) along on the trip. At the very least, a better awareness of all those organisms that exist under cover of their host is sure to lead to significant progress in the task of characterising all of Earth’s biota.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1186202 2017-08-24T12:57:01Z 2017-08-30T00:20:43Z Taxonomy 2028 Challenge: Let's digitally image all (or most) of our type specimens

 Posted on behalf of Kenny Travouillon, Curator of Mammalogy, Dept. of Terrestrial Zoology, Western Australian Museum


  1. By 2028 we will have digitalised the majority of type specimens in museum collections and made them available to researchers, industry and the general public.
  2. This will result in increased productivity of taxonomists, and make it easier to identify species in the field.  Several museums have already digitalised their type specimens and made them available on their website to the public, but achieving complete online access to all type data will help taxonomists recognise named species from new species more easily and also help create field guides, with keys to identify species in the field. This can not only be done for modern species, but also for fossil species, collected from more fragmented material.
  3. This matters because the taxonomic process is still a very slow process which requires years of research before making new species discovery. Yet, species are going extinct at an increasing rate, but many remain unnamed or have yet to be discovered. Digital access to type specimens will help speed up this process and get on with the job of conserving taxa earlier. Having a tool to make species identification in the field easier will also help researchers and industry with population monitoring. 
  4. Resources to achieve this will be funding to help institutions to hire additional staff to digitalise the collections, as well as IT staff to make this information available online for access by anyone. 
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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1185319 2017-08-21T05:25:59Z 2017-10-08T14:57:12Z The Taxonomy 2028 Challenge: Obtain high quality collections of all undescribed vascular plant taxa

New taxa continue to be discovered through examination of herbarium collections, regional surveys and botanical assessment of areas proposed for development; however, their taxonomic resolution and publication is often hampered by a lack of high quality (or even reasonable quality) material to serve as a type gathering or to enable the taxon to be adequately described. Many putative new taxa are represented by just one or a few collections that are fragmentary or lack key diagnostic features such as flowers or fruits.

By 2028 we will ensure that high quality collections of all undescribed vascular plant species (our known unknowns) will be made available for study in herbaria.

In the face of escalating threats to our biodiversity, there is a pressing need for a targeted collection effort to underpin taxonomic and systematic research, conservation planning and decision making. We need to act now or we risk undescribed species going extinct before they are adequately recorded. High quality collections can serve as type material and will enable reliable morphological descriptions to be generated, thereby facilitating accurate identification and on-ground conservation actions. Ancillary collections (e.g. samples for molecular studies, photographs, live material) could feed into other proposed 2028 goals (e.g. a genomic ark, stakeholder engagement) and ex situ conservation strategies.

For some undescribed species, obtaining good collections will be fraught with difficulties — many occur in remote or otherwise difficult to access areas, lack accurate geocode or locality information to enable them to be easily relocated, or require good seasonal conditions or fire to stimulate flowering. Furthermore, repeated visits to the same site may be required in order to collect adequate samples. We will therefore need skilled and energetic personnel to assess collection gaps, plan and conduct complex, targeted field expeditions or to otherwise co-ordinate regional personnel and skilled citizen scientists. Curatorial support will be essential for specimen processing, database and maintenance so that the specimens and their data can be made available for use by scientists.

An effort such as this would negate a major impediment to describing our vascular plant flora. And perhaps by the time this material is obtained, processed and ready for study, a future generation of skilled taxonomists with permanent positions will be in place and able to use these collections to best effect.


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Juliet Wege
tag:notobiotica.posthaven.com,2013:Post/1184571 2017-08-18T01:09:33Z 2017-08-18T01:21:24Z Taxonomy 2028 Challenge: A vision for fungal taxonomy and systematics

Posted on behalf of Alistair McTaggart, Postdoctoral Fellow, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria. Email: alistair.mctaggart@gmail.com

Web Pages: FABI profile (current employment), Google Scholar profileRust Fungi of Australia (taxonomy of rust fungi from prior post doc), Smut Fungi of Australia (taxonomy of smut fungi), Rust Fungi of Southern Africa (taxonomy of rust fungi in South Africa from current post doc)

Background

I am an early career researcher interested in the systematics of rust and smut fungi, which are both groups of plant pathogenic fungi. I dabble in the taxonomy of all other microfungi. I am currently based in South Africa and am being trained in genomics. I believe genomics is the best field to resolve the taxonomy and long-standing biological questions for my taxa of interest.

My answers largely reflect the field for taxonomy of fungi.


Where would you like taxonomy and systematics to be in a decade?

For pure taxonomy, I would like to see incorporation of new taxa into comprehensive, dynamic, public platforms, and an end to esoteric monographs. Taxonomy and application of a name should be accessible to everyone. This is possible through the development of public Lucid and Silverlight keys (here is an example of my friend Tim’s key to Carex in the United States: http://tinyurl.com/zjodnbb) that are open for collaboration within the community and are easy for non-experts to use. Single species descriptions are fine, but without incorporation into a bigger taxonomic picture, they pass by unnoticed. The community needs to embrace bigger picture treatments for their organisms. In the world of rust and smut fungi (and others), it’s already happening!

For systematics, I would like (and think it will happen) a total shift to phylogenomics, even if this means including a few loci of a taxon into a phylogenomic dataset. Cryptic species are rife in the mycological world and morphology only gets a taxonomist so far. Experts of a group rely on molecular barcodes and might not be able to make a confident identification of species (or genera) without molecular data. Mycologists have gradually progressed from single loci, to concordant and concatenated phylogenetic species hypotheses. Last year, we saw the first phylogenomic study of Zygomycota, which was casually published in a low-impact (but excellent quality) mycology journal. This will be the standard in the future. The sooner we get there, the sooner people will stop changing the taxonomy with every new gene they sequence. People working on genomic data will determine markers that may resolve a particular group, or markers that need to be included to determine populations, species, genera, families… The mycological community (at least) is going to have to embrace phylogenomics because this will happen within a decade (1K Fungal Genomes almost complete). This month I sequenced my first genome on a MinION (NanoPore™) with a desktop computer. In 10 years such a procedure will be less exciting for those taking part, and huge amounts of data will be at our fingertips.

What achievements or programs would you like to see in place?

Opportunities similar to the 1K Fungal Genomes project (or 10K Plant Genomes) for Australian taxa, particularly microorganisms.

High Performance Computing facilities made publicly available to researchers that need to work with large datasets (compare to the CHPC in South Africa).

Secure, electronic repositories to store genomic sequencing data before (and after) genomes are uploaded to public databases.

What innovations in technology, infrastructure, funding or organisation will make a big difference to your work and to our taxonomy and systematics?

  • Technology to sequence genomes from small amounts of starting material (such as Chromium 10X).
  • Desktop sequencing platforms (such as MinION).
  • Reduced cost of genome sequencing.
  • Access to electronic storage and high performance computing.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1184568 2017-08-18T00:40:57Z 2017-10-08T14:58:04Z Taxonomy 2028 Challenge: No net loss of FTE dedicated taxonomists

Posted on behalf of Dr Glenn Moore, Curator of Fishes, Department of Aquatic Zoology, Western Australian Museum


  1. By 2028 we will have no net loss of FTE dedicated taxonomists Australia-wide
  2. This will result in  security of taxonomic capacity and prevent the ‘brain drain’.
  3. This matters because there has been a well-documented global decline in dedicated taxonomists over the past few decades (eg Boero 2010; Disney 1998; Drew 2011).  This is despite the increasing need to understand the basic units of environmental, ecological, climate change and related research.  While much of the Decadal Plan is focussed on raising awareness of the role of taxonomy and its obvious importance to all fields of biological research, we also need to draw a line in the sand and stop any further reductions in taxonomic capacity in Australia.  We argue, with good reason, for increased staffing, training and students in the field, but this relies on increased funding.  The first step is to stop the decline, which already operates within funded models (at least to some degree).  Capacity needs to increase by 2028, but at the very least we must ensure it doesn’t decrease!
  4. Resources to achieve this will be recognition of the role of taxonomy, support from administrators, funding

Boero, F. (2010). The Study of Species in the Era of Biodiversity: A Tale of Stupidity. Diversity 2: 115.
Disney, H. (1998). Rescue plan needed for taxonomy. Nature394(6689), 120.
Drew, L. W. (2011). Are We Losing the Science of Taxonomy? As need grows, numbers and training are failing to keep up. BioScience61(12), 942-946.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1183755 2017-08-15T03:45:44Z 2017-09-04T00:30:21Z Taxonomy 2028 Challenge: Greater engagement with the public and end users of taxonomy

Taxonomy is a field that celebrates the immense diversity of life and allows for effective communication across not only scientific disciplines related to biology, but also for a whole range of other fields and industries that are crucial to our society (e.g. medicine, biosecurity, horticulture etc.). Its central role across these disciplines often goes unnoticed and in many cases underappreciated (e.g. Garnett & Christidis 2017). 

The level of success that we hope to achieve from our decadal plan (and indeed also with all subsequent plans after it) will invariably depend on the support of not only the systematic and scientific community, but also the larger community as a whole. Therefore, I propose that:

By 2028 we will achieve greater awareness, appreciation, and engagement from the wider public about the role and importance of taxonomy and systematics.

This will only result in outcomes that will inevitably benefit taxonomy and systematics which in turn contributes to the wider society. E.g. Greater funding (hopefully!) for taxonomic research and infrastructure development due to an increased appreciation and demand for taxonomic knowledge from the public.

Resources to achieve this will include:

First, broad surveys conducted during the start of the decadal plan followed by subsequent surveys at regular intervals (e.g. annually), allowing us to quantify and track our progress. Consultation and collaboration across the systematic society and social sciences would be particularly important in this case.

Similar initiatives have been noted, for example a survey was conducted during last year’s ASBS conference at Alice Springs targeted to our systematics community, and for botanical collections (e.g. the State Botanical Collection Significance Assessment, Royal Botanic Gardens Victoria 2016), though none has been conducted to the wider public at present.

With awareness comes appreciation, and with appreciation comes engagement – a crucial component for any endeavour. Questionaires can be constructed following this order:

1)   Awareness:

Example Q: Are you familiar with the fields of taxonomy and systematics? Y/N

Example Q: Are you aware of what a herbarium is? (*most people I’ve asked don’t!) Y/N

Example Q: Do you think herbaria and museums play a role in the fields of taxonomy and systematics? Y/N

Example Q: What do you think are the roles of a taxonomist or systematist?

2)   Appreciation:

Example Q: How important do you think the fields of taxonomy and systematics are to our society?

rank from 1–5 (for economic importance, scientific importance, cultural importance etc.)

Example Q: How important do you think the fields of taxonomy and systematics are in understanding and classifying the diversity of life?

rank from 1–5

3)   Engagement:

Example Q: Is the level of engagement of the taxonomic community with the broader public and end users sufficient?

rank from 1–5

Example Q: How can we improve our level of engagement?

The brief example above is targeted for the broader general public. Similar surveys can be created for specific groups of end users such as consultants, horticulturalists, or even other scientists who are not in the fields of taxonomy or systematics. Questions can be crafted following discussions and consultations with members of our community.

Establising a baseline survey will be critical in monitoring our progress. E.g. what percentage of the public is aware of the roles that taxonomists and systematists have?

In addition, these surveys will allow us to tailor our approach and invest in areas that we are currently lacking in terms of outreach (besides new species discoveries that attract the attention of the press and often quirky names that are associated with these new taxa [e.g. in Crisp et al. 2017], other roles of taxonomy often goes unnoticed – such as breakthroughs linked with evolutionary biology, phylogenetics, and biogeography).

Any potential differences noted across different levels of demography would be of particular interest  ­­–  especially on the responses of the younger generations (i.e. prospective and current students of biology).

Attracting and engaging younger generations in the fields of taxonomy and systematics is crucial to the survival of these disciplines. Engaging the younger demographic would require the use of media channels that they are regularly exposed to e.g. social media channels.

Noteworthy examples that utilises social media for taxonomic outreach include:

Novataxa: A blog dedicated to disseminating taxonomy and science, by featuring newly described species from across the planet in a way that is accessible to the wider public (by including pictures and summary diagnoses that can be understood by a layperson).

www.novataxa.blogspot.com.au

www.facebook.com/novataxa/

In other cases, personal blogs or social media sites (e.g. www.instagram.com/francisnge/) can also serve as an effective medium for taxonomic outreach.

Herbaria across Australia have their own dedicated social media sites on Facebook, and indeed one also exists for the Australian Systematic Botanical Society. Perhaps a site specifically dedicated to disseminating taxonomy and systematics should be created for the Australasian region, featuring the immense diversity that we have. A working model could include some of the features noted in Novataxa and In Defense of Plants ­­– a popular American botanical site aimed at engaging biology students (www.indefenseofplants.com; Fig. 1), it’s facebook site has garnered over 29000 likes www.facebook.com/InDefenseOfPlants/

Figure 1. Attracting a wider audience to what taxonomy and systematics entails – the study of the diversity of life.

A more active engagement from the public could aslo be achieved through these social media sites, for example the Kwongan foundation (www.facebook.com/kwonganfoundation/), a community site created for the conservation of Australia’s biodiversity with input from people across all regions, including those outside of Australia. Active participation from the community is maintained through engagement with other relevant groups that are present on social media e.g.

The Wildflower Society of Western Australia (currently with over 7000 online members; www.facebook.com/groups/129636970391772/)

and the Australian Native Plant Enthusiasts forum (currently with over 9000 online members; www.facebook.com/groups/675253642559682/)

Of course, engaging through the use of social media is only one way in getting our message across, and there are numerous ways of doing so, including increasingly novel ways that evolve with the development of increasingly sophisticated technologies (e.g. apps for plant identification). Nevertheless, it is a useful medium for which we can disseminate information through to a wider audience.

Finally, additional subsequent outreach strategies can be drafted, developed, and implemented following surveys conducted to the relevant stakeholders and consultation with the wider community.

Contributed to the Taxonomy 2028 Challenge by Francis Nge, University of Adelaide and State herbarium of South Australia

References:

Crisp, M.D., Cayzer, L., Chandler, G.T. & Cook, L.G. (2017). A monograph of Daviesia (Mirbelieae, Faboideae, Fabaceae). Phytotaxa 300(1): 1–308.

Garnett, S.T. & Christidis, L. (2017). Comment. Taxonomy anarchy hampers conservation. Nature 546 Issue 7656 (1st June 2017 ): 25–27.

 

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Francis Nge
tag:notobiotica.posthaven.com,2013:Post/1183174 2017-08-13T06:23:06Z 2017-08-24T02:56:21Z Taxonomy 2028 Challenge: a taxonomic emergency for vanishing coral reef fauna

The world’s coral reefs are facing imminent degradation from a variety of pressures. Current research suggests we have lost half of the world’s coral reefs in the last 30 years, and that reefs will disappear completely in the next 20-30 years. Despite this, the biodiversity of coral reefs is globally estimated to be represented by around 950,000 (±40%) multicellular species and only 10% of them have been described (Fisher et al. 2015). 

By 2028 we could double the number of described coral reef taxa.

This vision will result in a more comprehensive inventory for a fauna that we do not have the luxury of working steadily on for the next few decades. This is of great importance for a myriad of reasons, not least among which, coral reef organisms have contributed many new drugs that might preserve or improve human well-being.

This type of taxonomic emergency is something that scientists should come together to co-operate and speed up outcomes, before its too late.


[To be honest, I have no idea if this is achievable or not. It would require the description of 95,000 species in 10 years. Seems big. But achievable if big investment also occurs. And morally speaking, I think we should try!].


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Nerida Wilson
tag:notobiotica.posthaven.com,2013:Post/1181258 2017-08-11T07:55:38Z 2017-08-24T13:32:14Z Taxonomy 2028 Challenge: The Australian National Biodiversity Collection

Australia currently has around 100 public biodiversity collections (based on the ALA's Collectory pages), with a combined holding of >50 million specimens covering all organismic groups, and an estimated value of >$5 billion. In aggregate, the collection comprises a megascience infrastructure for biodiversity research in Australia, our region and the world, similar in scale and value to other megascience initiatives such as the Square Kilometre Array or the Large Hadron Collider.

However, the collection is jurisdictionally very scattered. In general, each state and territory has a large or relatively large herbarium and museum collection, under a variety of jurisdictional and reporting arrangements (e.g. from semi-autonomy under an independent Board to embedded in botanic gardens or various government departments). Some universities have collections, ranging from small teaching collections to substantial holdings. There is also a long tail of smaller, special-purpose collections in universities and various government departments. 

This jurisdictional scatter has arisen for obvious historical reasons: the establishment of the major herbaria and museums was mandated or facilitated under state and territory legislation; the CSIRO collections were established under its research mandate; and the smaller collections were established by universities and government departments for specific purposes not adequately covered by the major institutions.

Importantly, funding decisions that affect our collections are made by a very wide variety of budgeting agencies (from local to state or territory to national), with very little national coordination or strategy that can buffer a given collection from the exigencies of its local funding pressures.

Further, the wide scatter of collections means that few "owners" of collections see their collection as part of a megascience infrastructure, and nor does the community as a whole.

So, here's my vision:

By 2028, all our biodiversity collections will be integrated to form the Australian National Biodiversity Collection

The main goal of the ANBC will be to change the way governments, industry and the community view our individual collections - from seeing them in isolation to seeing them as part of something much greater. For obvious reasons, each individual institution will remain under local jurisdictional control and management. However, we will market our collections as e.g. "The xxxx collection, part of the Australian National Biodiversity Collection". 

We will establish an arrangement under the Council of Australian Governments (COAG) whereby the importance of each collection as part of the whole is acknowledged, including if possible negotiated agreements on minimal required baseline funding for each collection. 

We will also establish a strategic governance structure for the ANBC as a whole, to ensure strategic planning for the aggregate as well as individual collections, rather than for individual collections alone, and to increase recognition of the strategic value of each collection and of the ANBC in aggregate, in order to increase profile and funding.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1180425 2017-08-04T11:28:10Z 2017-08-31T04:12:50Z Taxonomy 2028 Challenge: Providing certainty in taxonomic applications through next generation sequencing

Holotypes are the universal standards we use to build our taxonomic knowledge. Since the integration of genetic data into our methods, our knowledge of diversity is rapidly increasing, but rarely can be linked back to species names. This has led to a divergence of knowledge systems where sometimes we have a parallel set of understanding that cannot be accurately tied together. In order to progress taxonomy, we need to be able to link all this new information with the centuries of foundational work based largely on morphology. Most holotypes are old, or preserved in a way that doesn’t easily allow the extraction of genetic information. However, newer technologies have overcome many of these issues (e.g. formalin preservation, degraded samples) and it should be possible to retrieve a barcode that could link historical type material with molecular studies.

By 2028 we will barcode 50% of holotypes in Australasian collections. This will result in the ability to link genetic information with available names and provide context for interpreting all molecular studies. This will solve some seemingly intractable taxonomic questions, and provide an essential resource for the future. This matters because currently, at best, molecular studies can include material re-collected from type localities, but most don’t, or can’t, since these areas may be highly impacted by human development. The proposed project will provide absolute certainty for contemporary identifications.

While it is not possible to utilise a single gene across all life, the key is unlocking the relevant marker for the groups of interest. Shotgun sequencing can be used to produce barcodes for type material. Shotgun sequencing breaks up DNA into small pieces, which get sequenced in short, overlapping fragments. These are assembled into continuous pieces, which will usually contain the high copy genes that we often use for species-level studies.

By maintaining project-level hubs at the involved institutions, existing databases will maintain the complete metadata record, while a purpose-built (very simple) database could list the species name and collection registration number. Using these two terms in a search of the public database GenBank, where data will be deposited, will retrieve all available data for that type. Other resources required would be salaries for project managers/scientists, a budget for sequencing, and the support of the involved institutions.

This project will increase the utility and integration of existing genetic information and provide absolute certainty of species-level identifications. It will also reduce the need for loaning or handling type material, which in many cases, becomes more fragile with age. This is future-proofing taxonomy!

By Nerida Wilson and Kym Abrams

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Kym Abrams